Lecture no. 2 basics of biochemistry -

basics of biochemistry

1. Introduction to biochemistry
AMNU 214

2. Course grade distribution
Final Exam
40%
Mid Term Exam
20%
Quizzes
20%
Assignments
20%
Total
100%

8. Proteins
Proteins are polymers of amino acids
Each has a unique 3D shape
Amino acid sequences vary
Proteins are major component of cell parts
The provide:
support and structural components
Several types of proteins are identified:
receptor, contractile, defense, enzymes,
structural

9. Building Blocks: Amino Acids
There are 20
different types
of amino acids
All have this
general formula
The R group is a
variable group

11. Polar vs. Non-polar Amino Acids
Some amino acids are polar while some are non-polar

12. Amino acids may be either polar or non-polar depending on the composition of their
side chain
Polar amino acids have hydrophilic R groups, while non-polar amino acids have
hydrophobic R groups

13. The localization of polar and non-polar amino acids will be determined by the
type of protein and its function:
Watersolubleproteins:
•Non-polaraminoacidstendtobefoundin
thecenterofthemolecule(stabilizethe
structure)
•Polaraminoacidstendtobelocatedonthe
proteinsurface(capableofinteractingwith
watermolecules)

15. Membrane-boundproteins:
•Non-polaraminoacidstendtobe
locatedontheregionsofthesurfacein
contactwiththemembrane
•Polaraminoacidswillgenerallyline
interiorpores(tocreatehydrophilic
channels)

16. Significance of polar & non-polar amino acids
polar amino acids non-polar amino acids
Hydrophilic
can make hydrogen bonds
found in hydrophilic
channels & parts of proteins
projecting from membranes
found on surface of water-
soluble proteins
hydrophobic
forms van derWaals
(hydrophobic interactions)
with other hydrophobic amino
acids
found in proteins in interior of
membranes
found in interior of water-
soluble proteins

17. Peptide Bonds
Proteins are formed
by condensation
A peptide bondis
formed

18. Four levels of protein structure

19. Primary Structure
Primary structure is a
chain of amino acids
number & unique
sequence of amino acids
determine the properties
of primary structure
each position is occupied
by one of 20 different
amino acids
sequence of amino acids
is determined by DNA
sequence in genes
linked by peptide bonds

20. Secondary structure
formed by interaction
between amino and carboxyl
i.e. -NH and -C=O groups
weak hydrogen bonds are
formed between –H & = O
there are two types: a-helix
and b-sheet
α-helix formed / polypeptide
coils up e.g. sheep wool
β-pleated sheet formed e.g.
silk in spider web
regular repeated folding of
amino acid chain
secondary structure is
stabilized by hydrogen bonds

21. Tertiary structure
These are globular proteins
with irregular conformation
tertiary structure is the
folding up of the polypeptide
chain, secondary structure or
alpha helix
it gives three dimensional
globular shape i.e. shape of
active site
the structure is stabilized by
disulphide bridges, hydrogen,
ionic& hydrophobic bonds
tertiary structure used as
enzymes to catalyze
biochemical reactions

22. Quaternary structure
made of several
polypeptide subunits
joined together
they maybe conjugated
proteins i.e. proteins
which combine with a
prosthetic group (non-
protein molecules)
prosthetic groups
includes: metals e.g. iron
in haemoglobin, nucleic
acids as in ribosomes ,
carbohydrates as in
glycoprotein or lipids as
in glycolipids

23. Denaturation of Proteins
change in protein’s
usual regular
structure due to:
High temp
Change in pH
Addition of organic
solvent (alcohol,
acetone)
These factors break
the bonds that
stabilize the
structure

24. Protein Functions
Function Examples
Structure
Transport
Enzymes
Movement
Hormones
Antibodies
storage
–collagen/keratin/fibrin
–myoglobin/hemoglobin, bind &
transport oxygen
–lysozyme, speeding up metabolic
reactions
–actin(and myosin tropomyosin(and
troponin)
–insulin,regulate blood glucose
–immunoglobulin
–albumin in egg, casein in milk